From owner-chemistry@ccl.net Wed Jan 4 13:44:00 2012 From: "Barbara Fresch bfresch++ulg.ac.be" To: CCL Subject: CCL:G: starting guess from unrestricted DFT for CAS-SCF in G09 Message-Id: <-46111-120104123908-11514-WH5Ot1LEgx23bcA5RJ0LNw : server.ccl.net> X-Original-From: "Barbara Fresch" Date: Wed, 4 Jan 2012 12:39:03 -0500 Sent to CCL by: "Barbara Fresch" [bfresch^-^ulg.ac.be] hello everybody, i'm trying to obtain the CASSCF wavefunction of the ground state of a metal cluster with G09. I want to select the active space from the orbitals obtained by an unrestricted B3LYP optimization. I can also use those orbitals as starting guess for the CASSCF (I just use Guess=Read). Here where I'm confused: since from the unrestricted-DFT one obtains two set of orbitals (the alpha and the beta orbitals) while as far as i understood the CASSCF wavefunction is a combination of restricted determinants, how the initial guess is adapted? Does Gaussian use only e.g. the alpha set of orbitals? thanks in advance for your help. Barbara Fresch e-mail: bfresch\a/ulg.ac.be From owner-chemistry@ccl.net Wed Jan 4 14:19:00 2012 From: "rocky walden rocky.walden19{:}gmail.com" To: CCL Subject: CCL: Script for MD simulation Results Message-Id: <-46112-120104091652-27931-2Qergr/O4i9bYJNCuk4H3w^server.ccl.net> X-Original-From: rocky walden Content-Type: multipart/alternative; boundary=20cf303b414d49533e04b5b477a8 Date: Wed, 4 Jan 2012 19:46:46 +0530 MIME-Version: 1.0 Sent to CCL by: rocky walden [rocky.walden19]*[gmail.com] --20cf303b414d49533e04b5b477a8 Content-Type: text/plain; charset=ISO-8859-1 Hi CCL Users, I have run some Replica Exchange MD simulations using IMPACT code, I am able to view the trajectory, which shows the moment of the bonds with respect to time. I would like some one to guide me to write a python script, where i can input the trajectory data so that I would get an output displayed in 2D graph, ideally PotEnergy vs time, or PotEnergy vs temp.... I would really appreciate if someone helps me out in this. Have a wonderful year 2012, with good health, and happiness. Thanks Rocky.W --20cf303b414d49533e04b5b477a8 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi CCL Users,

=A0=A0=A0=A0 I have run some Replica Exchange MD simul= ations using IMPACT code, I am able to view the trajectory, which shows the= moment of the bonds with respect to time.
=A0=A0=A0=A0 I would like som= e one to guide me to write a python script, where i can input the trajector= y data so that I would get an output displayed in 2D graph, ideally=A0 PotE= nergy=A0 vs time, or PotEnergy vs temp....

=A0=A0=A0=A0=A0 I would really appreciate if someone helps me out in th= is.

=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Have a wonderful year 20= 12, with good health, and happiness.
Thanks
Rocky.W
--20cf303b414d49533e04b5b477a8-- From owner-chemistry@ccl.net Wed Jan 4 17:23:00 2012 From: "Emilio Gallicchio emilio^^^biomaps.rutgers.edu" To: CCL Subject: CCL: Script for MD simulation Results Message-Id: <-46113-120104155048-30161-U49d8D+91G0BKszqQcBcmA:server.ccl.net> X-Original-From: Emilio Gallicchio Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 4 Jan 2012 15:50:42 -0500 MIME-Version: 1.0 Sent to CCL by: Emilio Gallicchio [emilio%a%biomaps.rutgers.edu] Rocky, I assume IMPACT REMD was performed within Schródinger's environment > from the Maestro GUI? I believe the system automatically unscrambles the replica trajectories so that all of the frames at one temperature appear in the same file. This procedure basically destroys time ordering. I would recommend contacting Schródinger to see if there's an easy way to turn off this behavior. If this issue doesn't affect you, below is a sample python script to read an Impact trajectory and extract data from it. Best, Emilio --  Dr. Emilio Gallicchio  Director of High Performance Computing  BioMaPS Institute - Rutgers University  Wright-Rieman Laboratories Room 205  610 Taylor Rd.  Piscataway, NJ  08854-8087  Email: emilio(0)biomaps.rutgers.edu  WWW: http://hpcp.rutgers.edu/~emilio  Phone: 732-445-5157   Fax: 732-445-5958 #-------------------------------------------------------------------------------------------------------- > from schrodinger import structure, structureutil > from schrodinger.trajectory.cmsstructure import CmsStructure > from schrodinger.trajectory.desmondsimulation import DesmondSimulation cmsfile = 'r24_t300.000000k.mae' trjfile = 'r24_t300.000000k.trj' csim = DesmondSimulation(cmsfile, trjfile) print 'Number of frames:', csim.total_frame for i in range(csim.total_frame-1): ct1 = csim.getFrameStructure(i) temp = ct1.property['r_i_target_temperature'] e = ct1.property['r_i_Potential_Energy-OPLS2005'] print i, temp, e On Wed, Jan 4, 2012 at 9:16 AM, rocky walden rocky.walden19{:}gmail.com wrote: > Hi CCL Users, > >      I have run some Replica Exchange MD simulations using IMPACT code, I am > able to view the trajectory, which shows the moment of the bonds with > respect to time. >      I would like some one to guide me to write a python script, where i can > input the trajectory data so that I would get an output displayed in 2D > graph, ideally  PotEnergy  vs time, or PotEnergy vs temp.... > >       I would really appreciate if someone helps me out in this. > >               Have a wonderful year 2012, with good health, and happiness. > Thanks > Rocky.W